Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g01793.M2

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 5133
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28


Found at i:3334 original size:12 final size:12

Alignment explanation


    Indices: 3317--3357  Score: 55
    Period size: 12  Copynumber: 3.4  Consensus size: 12

       3307 TGATGAGGAG

                    *   
       3317 GAAGAGGAAGAT
          1 GAAGAGGATGAT

                       *
       3329 GAAGAGGATGAG
          1 GAAGAGGATGAT

              *         
       3341 GATGAGGATGAT
          1 GAAGAGGATGAT

                 
       3353 GAAGA
          1 GAAGA

       3358 TGATCCTGGG


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  12   24  1.00

ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12


Consensus pattern (12 bp):   
GAAGAGGATGAT

Found at i:3335 original size:18 final size:18

Alignment explanation


    Indices: 3308--3342  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3298 AGAATCGGAT

                 *            
       3308 GATGAGGAGGAAGAGGAA
          1 GATGAAGAGGAAGAGGAA

                       *     
       3326 GATGAAGAGGATGAGGA
          1 GATGAAGAGGAAGAGGA

       3343 TGAGGATGAT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.43, C:0.00, G:0.49, T:0.09


Consensus pattern (18 bp):   
GATGAAGAGGAAGAGGAA

Found at i:3707 original size:18 final size:18

Alignment explanation


    Indices: 3686--3731  Score: 65
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       3676 AGATGGGGTA

                    *     *   
       3686 GAGGATGATGATGAGGAG
          1 GAGGATGAGGATGAAGAG

                              
       3704 GAGGATGAGGATGAAGAG
          1 GAGGATGAGGATGAAGAG

                 *    
       3722 GAGGAAGAGG
          1 GAGGATGAGG

       3732 TAGATAATGA


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   25  1.00

ACGTcount: A:0.37, C:0.00, G:0.52, T:0.11


Consensus pattern (18 bp):   
GAGGATGAGGATGAAGAG

Found at i:4016 original size:3 final size:3

Alignment explanation


    Indices: 4008--4067  Score: 120
    Period size: 3  Copynumber: 20.0  Consensus size: 3

       3998 GACCCAGGGA

                                                                           
       4008 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG

                           
       4056 ATG ATG ATG ATG
          1 ATG ATG ATG ATG

       4068 TAGAAGAGGA


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   57  1.00

ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33


Consensus pattern (3 bp):   
ATG

Done.